A capacitor structure and a manufacturing method thereof are disclosed in this invention. The capacitor structure includes a first electrode, a second electrode, and a capacitor dielectric stacked layer. The capacitor dielectric stacked layer is disposed between the first electrode and the second electrode, and the capacitor dielectric stacked layer includes a first dielectric layer. The first dielectric layer includes a first zirconium oxide layer and a first zirconium silicon oxide layer. A manufacturing method of a capacitor structure includes the following steps. A capacitor dielectric stacked layer is formed on a first electrode, and the capacitor dielectric stacked layer includes a first dielectric layer. The first dielectric layer includes a first zirconium oxide layer and a first zirconium silicon oxide layer. Subsequently, a second electrode is formed on the capacitor dielectric stacked layer, and the capacitor dielectric stacked layer is located between the first electrode and the second electrode.